R/FISH-109

Impact/Outcome:

They Are What They Eat: New Genomic Tools Help Define the Relationship Between Zooplankton Prey Quality and Fish Recruitment

Recap: Maryland Sea Grant-supported researchers used the novel method of genomic meta-barcoding to more precisely identify zooplankton species, as well as the contents of larval fish guts, in samples from the Choptank River. The work will help scientists and managers better understand the key relationship between zooplankton type, abundance, and diversity and fish recruitment.

Relevance: Zooplankton are a foundation of the Chesapeake Bay’s food webs. These mostly microscopic animals are a vital food source for larval fish (though fish larvae themselves are considered plankton at this stage of their lives). Yet, despite their importance to the growth and recruitment of species such as striped bass, scientists face challenges in understanding the relationship between zooplankton diversity and fish productivity. Identifying zooplankton species can be difficult and time consuming, as is understanding which are the highest quality and most frequently chosen prey among different larval fish, and how environmental factors—such as water quality and effects of climate change—influence zooplankton abundance and diversity. Finding a more efficient way to accurately identify zooplankton to assess diversity and abundance, as well as learning which fish are eating what zooplankton and when, can help fisheries managers better understand the key relationship between zooplankton and fish recruitment. 

Response: Between April and September over two years, researchers—including a Sea Grant Fellow and five undergraduates from Chesapeake College—took zooplankton and larval fish samples at three Choptank River sites near Maryland Department of Natural Resources water quality monitoring stations. They extracted 52zooplankton DNA samples and analyzed them via genomic metabarcoding, through which multiple species in a single sample can be genetically identified based on their unique DNA sequences. Researchers identified as many as 347 distinct taxa, including so-called cryptic species—those that look identical but are genetically different. Researchers also compared novel metabarcoding to traditional morphological species identification in terms of time, cost, and accuracy. The next step—using metabarcoding to precisely analyze larval fish gut contents and help determine feeding selectivity—is underway (COVID-19 restrictions delayed this research in 2020).

Result: The comparison of identification methods found that while both showed about the same taxonomic resolution, metabarcoding resulted in more identification to the species level than traditional morphological identification. Also, while metabarcoding costs slightly more, it requires far less time to process samples. The research confirmed that as DNA sequence databases expand, metabarcoding can help scientists more quickly and precisely identify zooplankton species and diversity in the Bay. The Sea Grant Fellow is developing a web-based application to help users analyze which identification process will work best for their project based on parameters including processing time and materials cost. Researchers plan to share their results at a 2021 workshop with federal and state fisheries officials, as well as develop a best-practices document on these methods. This research also established a new partnership with Chesapeake College that gives undergraduates long-term field and lab experience with cutting-edge molecular technologies in zooplankton and fisheries ecology.